Thank you both for providing a solution.
I have found an even easier way to work around this issue. (Certificate creation works, Renewal still using ACMEv01, not sure why!)
The latest Let's Encrypt i-MSCP plugin is using certbot 0.26.1 which is already capable of using ACMEv2. But it is not used by default.
You can change that by uncommenting line 796 in /var/www/imscp/gui/plugins/LetsEncrypt/backend/LetsEncrypt.pm so it looks like this:
Please keep in mind, that this files gets overwritten, when reinstalling or updating the Let's Encrypt Plugin.